Abstract Urbanization transforms natural river channels, and surface water of some rivers disappeared over time. How and whether the subsurface domains of the original waterways and aquifers connecting them (a phantom of historical landscape) are functional is not known. This study examined the effects of tributary groundwater inflow on the response of river–riparian organisms in an alluvial mainstem river in northern Japan, where the tributary disappeared over the course of urban landscape transformation. A 2.8‐km lowland segment of the mainstem gravel‐bed river was examined for water properties and the river–riparian food web. In addition, watershed‐wide water sampling was conducted to isotopically distinguish several types of groundwater that contributed to the hyporheic water in the study segment. Altitude had a clear effect on the hydrogen/oxygen stable isotope ratios in the river water collected across the watershed. Groundwater unique both in chemical and isotopic signatures occurred in several spots within the study segment, and its properties resembled and its upwelling locations matched groundwater from a tributary river whose surface channel disappeared 60 years ago. Positive numerical increases in abundance and/or a sign of nitrogen transfer in river–riparian communities (algae, invertebrates and riparian trees) originating from groundwater high in nitrate with elevated nitrogen stable isotope ratios were found. We demonstrated that tributary groundwater with unique chemical properties manifested by an urban watershed river network continued to have trophic effects on biota across the river–riparian boundary in the mainstem river, even after urbanization transformed the tributary into a phantom river. We highlighted the legacy effects of landscape transformation in the subsurface domain and the significance of scrutinizing the past landscape and hydrological connectivity at the watershed scale in urban environments.